How can I remove a node group from my startup file?
Steps:


Open up a new Blender file (aka. the startup file)
In the Outliner, select "Data-Blocks" from the drop-down menu
Find the "Node Groups" section, which should contain the node groups that you are trying to remove
Expand one of the node groups and uncheck the "Fake User" field
Repeat this for all the node groups that you want to remove
Save the file as the start up file, close and open a new Blender file


The node groups that do not have any users will not be saved and thus will not be there when the startup file is loaded. If you have multiple node groups to remove and they have dependencies upon each other, then it may be necessary to save the startup file, close, open new, and save again a couple of times. Each time, the node groups without any dependencies (leaves) will be pruned and eventually you can remove all unwanted node groups.